[English] 日本語
Yorodumi
- PDB-6w1f: Crystal structure of Streptococcus thermophilus SHP pheromone rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w1f
TitleCrystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 bound to DNA
Components
  • (DNA (30-MER)) x 2
  • Positive transcriptional regulator MutR family
KeywordsDNA BINDING PROTEIN/DNA / TRANSCRIPTIONAL REGULATOR / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HTH-type transcriptional regulator Rgg, C-terminal domain / Transcription activator MutR, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Positive transcriptional regulator MutR family
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
Streptococcus thermophilus CNRZ1066 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNeiditch, M.B. / Capodagli, G.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125452 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure-function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay.
Authors: Glenn C Capodagli / Kaitlyn M Tylor / Jason T Kaelber / Vasileios I Petrou / Michael J Federle / Matthew B Neiditch /
Abstract: Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in species, controlling virulence, ...Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in species, controlling virulence, antimicrobial resistance, and biofilm formation. Rgg2 and Rgg3 function is regulated by their interaction with oligopeptide quorum-sensing signals called short hydrophobic peptides (SHPs). The molecular basis of Rgg-SHP and Rgg-target DNA promoter specificity was unknown. To close this gap, we determined the cryoelectron microscopy (cryo-EM) structure of Rgg3 bound to its quorum-sensing signal, SHP3, and the X-ray crystal structure of Rgg3 alone. Comparison of these structures with that of an Rgg in complex with cyclosporin A (CsA), an inhibitor of SHP-induced Rgg activity, reveals the molecular basis of CsA function. Furthermore, to determine how Rgg proteins recognize DNA promoters, we determined X-ray crystal structures of both Rgg2 and Rgg3 in complex with their target DNA promoters. The physiological importance of observed Rgg-DNA interactions was dissected using in vivo genetic experiments and in vitro biochemical assays. Based on these structure-function studies, we present a revised unifying model of Rgg regulatory interplay. In contrast to existing models, where Rgg2 proteins are transcriptional activators and Rgg3 proteins are transcriptional repressors, we propose that both are capable of transcriptional activation. However, when Rgg proteins with different activation requirements compete for the same DNA promoters, those with more stringent activation requirements function as repressors by blocking promoter access of SHP-bound conformationally active Rgg proteins. While a similar gene expression regulatory scenario has not been previously described, in all likelihood it is not unique to streptococci.
History
DepositionMar 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Positive transcriptional regulator MutR family
B: Positive transcriptional regulator MutR family
E: DNA (30-MER)
F: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)84,9264
Polymers84,9264
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-75 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.790, 90.790, 245.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 4 - 283 / Label seq-ID: 4 - 283

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

#1: Protein Positive transcriptional regulator MutR family


Mass: 33242.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Strain: ATCC BAA-250 / LMG 18311 / Gene: stu1044 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4D0
#2: DNA chain DNA (30-MER)


Mass: 9078.907 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptococcus thermophilus CNRZ1066 (bacteria)
#3: DNA chain DNA (30-MER)


Mass: 9363.046 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptococcus thermophilus CNRZ1066 (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 170 mM ammonium acetate, 85 mM sodium citrate, 22% PEG 4,000, and 15% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 18799 / % possible obs: 99.5 % / Redundancy: 10.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Χ2: 0.699 / Net I/av σ(I): 35.4 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.2610.30.6649280.8960.2160.6990.46399.9
3.26-3.3110.10.5579340.9090.1830.5870.47999.8
3.31-3.38100.5129590.9310.170.540.48699.9
3.38-3.459.30.3889010.9560.1340.4110.58497.6
3.45-3.529.70.3079420.9710.1030.3250.51599.7
3.52-3.610.80.2349430.980.0740.2450.508100
3.6-3.6910.70.2019450.9910.0640.2110.59100
3.69-3.7910.70.1739330.9920.0550.1810.592100
3.79-3.9110.60.1489490.9940.0480.1550.689100
3.91-4.0310.60.1169350.9950.0370.1220.69100
4.03-4.1810.50.1069410.9970.0340.1110.717100
4.18-4.3410.40.0899580.9960.0290.0930.829100
4.34-4.549.40.0759160.9970.0260.0790.91696.5
4.54-4.7810.60.0729340.9980.0230.0750.93999.9
4.78-5.0810.90.0669400.9980.0210.0690.934100
5.08-5.4710.80.0629390.9990.020.0650.759100
5.47-6.0210.60.069570.9980.020.0630.854100
6.02-6.899.50.0529280.9980.0180.0550.89398.4
6.89-8.6710.80.049490.9990.0130.0420.875100
8.67-5010.20.0319680.9970.010.0320.64698.9

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YV6

4yv6


Resolution: 3.2→45.395 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.77
RfactorNum. reflection% reflection
Rfree0.2662 1860 9.93 %
Rwork0.2168 --
obs0.2217 18729 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 341.18 Å2 / Biso mean: 151.7834 Å2 / Biso min: 86.51 Å2
Refinement stepCycle: final / Resolution: 3.2→45.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 1230 0 6 5842
Biso mean---110.45 -
Num. residues----620
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1688X-RAY DIFFRACTION6.656TORSIONAL
12B1688X-RAY DIFFRACTION6.656TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.28610.40681430.29271290100
3.2861-3.38270.33991470.28411319100
3.3827-3.49190.37681410.2768129698
3.4919-3.61660.27911360.22481284100
3.6166-3.76140.26851480.24311301100
3.7614-3.93250.32461410.25341314100
3.9325-4.13970.26981460.23651294100
4.1397-4.39880.24931400.21661292100
4.3988-4.73810.25831420.1984127398
4.7381-5.21430.29041440.20911302100
5.2143-5.96740.30381470.22881305100
5.9674-7.51280.27151390.2422130199
7.5128-45.3950.21451460.178129898
Refinement TLS params.Method: refined / Origin x: -19.406 Å / Origin y: 32.399 Å / Origin z: -25.426 Å
111213212223313233
T1.6917 Å20.507 Å2-0.143 Å2-1.04 Å2-0.0822 Å2--0.5239 Å2
L4.1082 °21.4772 °2-1.3653 °2-2.2881 °2-0.7556 °2--0.7054 °2
S0.4597 Å °0.5978 Å °-0.4348 Å °0.653 Å °-0.2011 Å °-0.2871 Å °-0.4255 Å °-0.2491 Å °-0.1827 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )A4 - 283
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )A301 - 302
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )B301 - 302
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )B4 - 283
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )E101
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )E1 - 30
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )F101
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:283 OR RESID 301:302 ) ) OR ( CHAIN B AND ( RESID 301:302 OR RESID 4:283 ) ) OR ( CHAIN E AND ( RESID 101:101 OR RESID 1:30 ) ) OR ( CHAIN F AND ( RESID 101:101 OR RESID 1:30 ) )F1 - 30

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more